Responses of apple cultivars and stock in vitro for viruses elimination by different heat therapy regime in combination with tip propagation were studied. The results showed that great differences were noted between materials in their tolerance of heat. Resistance of "Fuji" was stronger than that of Malus xiaojinensis, and "Stark Delicious" suffered from constant heat therapy. However, Diurnal alternating temperature treatment availed to prolong survival rate of plants throughout the whole period of treatment, which led to 0% death rate. When the length of shoot tips was about 1mm, the percentage of viable apexes did not obviously correlated with materials, regimes or days of heat therapy, but possibly correlated with its surround conditions such as temperature. Rates of virus-elimination under same treatment differed from plant to plant. M. xiaojinensis listed the top followed by "Fuji", while "Stark Delicious" ranked number three. However, viruses were always inactivated in the same order: first apple chlorotic leaf spot virus (ACLSV), followed by apple stem grooving virus (ASGV). Concerning about death rate of materials during heat treatment and virus elimination rate, 20-day constant heat treatment or 30-day alternating temperature therapy was effective for M. xiaojinensis to eliminate ACLSV and ASGV. Virus-free plant of "Fuji" favorite resulted from 30-day constant heat treatment or alternating temperature therapy with treatment period of more than 30 days. But for "Stark Delicious", an alternating temperature therapy regime was more suitable.